IntroductionThe FMS-related tyrosine kinase-3 (FLT3) is a receptor tyrosine kinase expressed in early hematopoietic progenitors that plays an important role in hematopoietic development. 1,2 Multiple studies have shown that activating mutations of FLT3 are common in blasts from patients diagnosed with acute myelogenous leukemia (AML) but are rarely found in adult patients with acute lymphoblastic leukemia (ALL). [2][3][4] We have recently shown that FLT3 is consistently highly expressed in MLL rearranged acute lymphoblastic leukemias (MLLs). 5 This prompted analysis for FLT3 mutations in MLL, where we found approximately 15% contain activating mutations in the receptor activation loop. 6 A large gene expression analysis of childhood ALL samples has shown that high-level FLT3 expression is also found in ALL samples containing more than 50 chromosomes (hyperdiploid ALL). 7 Here we show that activating FLT3 mutations are found in diagnostic specimens from 6 of 25 patients with hyperdiploid ALL, but only 1 of 29 patients with TEL/AML1-rearranged ALL. Also, 3 of 16 patients with leukemia who would ultimately have a relapse harbored FLT3 mutations. Most of the mutations are previously described activation loop mutations, but 4 are new mutations consisting of either small deletions or insertions in the juxtamembrane region of the receptor. These data suggest that patients with hyperdiploid or relapsed ALL should be considered possible candidates for therapy with recently described small-molecule FLT3 inhibitors. [8][9][10][11] Study design Patient samplesLeukemia samples were obtained from either bone marrow or peripheral blood at diagnosis from patients with ALL. The peripheral blood samples all had more than 10% blasts at diagnosis. Patients were treated according to Dana Farber Cancer Institute protocols 91-001, 95-001, and 00-001. Informed consent was obtained from all patients after approval of the Institutional Review Board. Standard cytogenetic analysis was performed on all samples. TEL-AML1 translocations were determined by florescence in situ hybridization (FISH) or polymerase chain reaction (PCR) as previously described. 12 Mutation detectiongDNA was extracted from leukemia samples with Trizol (Invitrogen, Carlsbad, CA). Mutations in the juxtamembrane domain were identified by amplifying a region spanning exons 14 and 15 with primers 14F (TGTA-AAACGACGGCCAGTCAATTTAGGTATGAAAGCC) and 15R (GAG-GAAACAGCTATGACCCTTTCAGCATTTTGACGGCAACC). The upstream primer in this reaction was fluorescently labeled (6-FAM) to allow sizing of all products when electrophoresed on a sequencing apparatus (Model 377, Applied Biosystems, Foster City, CA). The area under the curve of a variant product was divided by the total area under all curves to approximate the percentage of variant alleles in a sample. When variant products were determined to constitute more than 30% of the signal, the sample was directly sequenced following the initial PCR. Samples with no detectable length mutations were also directly sequenced. For a sample with ...

Hybrid rice is the dominant form of rice planted in China, and its use has extended worldwide since the 1970s. It offers great yield advantages and has contributed greatly to the world’s food security. However, the molecular mechanisms underlying heterosis have remained a mystery. In this study we integrated genetics and omics analyses to determine the candidate genes for yield heterosis in a model two-line rice hybrid system, Liang-you-pei 9 (LYP9) and its parents. Phenomics study revealed that the better parent heterosis (BPH) of yield in hybrid is not ascribed to BPH of all the yield components but is specific to the BPH of spikelet number per panicle (SPP) and paternal parent heterosis (PPH) of effective panicle number (EPN). Genetic analyses then identified multiple quantitative trait loci (QTLs) for these two components. Moreover, a number of differentially expressed genes and alleles in the hybrid were mapped by transcriptome profiling to the QTL regions as possible candidate genes. In parallel, a major QTL for yield heterosis, rice heterosis 8 (RH8), was found to be the DTH8/Ghd8/LHD1 gene. Based on the shared allelic heterozygosity of RH8 in many hybrid rice cultivars, a common mechanism for yield heterosis in the present commercial hybrid rice is proposed.

B cell lineage acute lymphoblastic leukemia (ALL) arises in virtually all cases from B cell precursors that are arrested at pre–B cell receptor–dependent stages. The Philadelphia chromosome–positive (Ph+) subtype of ALL accounts for 25–30% of cases of adult ALL, has the most unfavorable clinical outcome among all ALL subtypes and is defined by the oncogenic BCR-ABL1 kinase and deletions of the IKAROS gene in >80% of cases. Here, we demonstrate that the pre–B cell receptor functions as a tumor suppressor upstream of IKAROS through induction of cell cycle arrest in Ph+ ALL cells. Pre–B cell receptor–mediated cell cycle arrest in Ph+ ALL cells critically depends on IKAROS function, and is reversed by coexpression of the dominant-negative IKAROS splice variant IK6. IKAROS also promotes tumor suppression through cooperation with downstream molecules of the pre–B cell receptor signaling pathway, even if expression of the pre–B cell receptor itself is compromised. In this case, IKAROS redirects oncogenic BCR-ABL1 tyrosine kinase signaling from SRC kinase-activation to SLP65, which functions as a critical tumor suppressor downstream of the pre–B cell receptor. These findings provide a rationale for the surprisingly high frequency of IKAROS deletions in Ph+ ALL and identify IKAROS-mediated cell cycle exit as the endpoint of an emerging pathway of pre–B cell receptor–mediated tumor suppression.

In a prospective trial in 284 children with B-lineage acute lymphoblastic leukemia (ALL), we assessed the clinical utility of real-time quantitative polymerase chain reaction analysis of antigen receptor gene rearrangements for detection of minimal residual disease (MRD) to identify children at high risk of relapse. At the end of induction therapy, the 5-year risk of relapse was 5% in 176 children with no detectable MRD and 44% in 108 children with detectable MRD (P < .001), with a linear association of the level of MRD and subsequent relapse. Recursive partitioning and clinical characteristics identified that the optimal cutoff level of MRD to predict outcome was 10 ؊3 . The 5-year risk of relapse was 12% for children with MRD less than one leukemia cell per 10 3 normal cells (low MRD) but 72% for children with MRD levels greater than this level (high MRD) (P < . IntroductionModern multiagent anticancer drugs and risk-stratification treatment have made childhood acute lymphoblastic leukemia (ALL) the most successful example of a curable cancer. [1][2][3][4] In 4 consecutive clinical trials conducted by Dana-Farber Cancer Institute (DFCI) ALL Consortium (a complete list of the members of the Dana Farber Cancer Institute ALL Consortium is provided in Document S1, available on the Blood website; see the Supplemental Materials link at the top of the online article). Between 1981 and 1995, the 5-year event-free survival improved from 74% (Ϯ 3%) to 83% (Ϯ 2%). 5,6 Identification of clinical and biologic features associated with poor outcome allowed introduction of a riskadjusted strategy. 7 It remains important to evaluate novel risk factors to predict outcome so that therapy can be changed for children at high risk of relapse and potentially to decrease toxicity for children in whom less intensive therapy might be administered.Children in complete remission (CR) can have up to 10 10 leukemic cells, [8][9][10] and with one exception, 11 studies in childhood ALL have demonstrated the prognostic significance of detection and quantification of minimal residual disease (MRD). 12-19 MRD assessment from as early as 2 weeks after starting therapy predicts outcome, 20,21 with additional information obtained by multiple time points analyses. 14,22 Three methods are widely used for monitoring MRD, multiparameter flow cytometric analysis, 8,10 and polymerase chain reaction (PCR) amplification of either fusion transcripts, 23 or of the antigen receptor rearrangements for immunoglobulin (Ig) or the T-cell receptors (TCR). 14,15 PCR amplification of Ig and TCR rearrangements is limited by oligoclonality and clonal evolution, [24][25][26] but is widely applicable and has high sensitivity. Difficulties in quantification of MRD reproducibly can be overcome by real-time quantitative (RQ)-PCR, using consensus probes for framework 27,28 or joining regions. 29 The clinical utility of RQ-PCR has been reported to date in only small numbers of children. 25,[30][31][32][33][34] In this prospective study, we report on the clinical utility of ...